scholarly journals Distribution of COVID-19 and Phylogenetic Tree Construction of SARS-CoV-2 in Indonesia

2020 ◽  
Vol 14 (suppl 1) ◽  
pp. 1035-1042
Author(s):  
Dora Dayu Rahma Turista ◽  
Aesthetica Islamy ◽  
Viol Dhea Kharisma ◽  
Arif Nur Muhammad Ansori
Keyword(s):  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Case Fatality ◽  
Medical Personnel ◽  
Distribution Data ◽  
Cure Rate ◽  
Transmission Process ◽  
Tree Construction ◽  
The World ◽  
History Of

Coronavirus disease 2019 (COVID-19) is a disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 has spread quickly across the world and has been declared a pandemic. Indonesia has many COVID-19 cases, with a high mortality rate. This study aimed to describe the distribution of COVID-19 in Indonesia and constructed the SARS-CoV-2 phylogenetic tree from Indonesian isolates and those from other countries, including other CoVs to determine their relationship. The distribution data of COVID-19 in Indonesia were obtained from the COVID-19 Management Handling Unit and descriptively analyzed. SARS-CoV-2 isolates were retrieved from the GenBank® (National Center of Biotechnology Information, USA) and GISAID EpiCoV™ databases and were used to construct phylogenetic trees using MEGA X software. Of the 37 provinces in Indonesia, five provinces with the highest case fatality rates were DKI Jakarta, Jawa Barat, Jawa Timur, and Banten, and the five provinces with the highest cure rate were Kepulauan Riau, Bali, Aceh, Gorontalo, and DI Yogyakarta. SARS-CoV-2 Indonesian isolates were closely related to SARS-CoV-2 isolates from other countries. The rapid and widespread distribution of SARS-CoV-2 in Indonesia was caused by the lack of compliance with territorial restrictions and dishonesty with medical personnel. These data revealed that mutations can occur during the transmission process, which can be caused by a history of travel and increased patient immunity.

INFERRING PHYLOGENETIC RELATIONSHIPS AVOIDING FORBIDDEN ROOTED TRIPLETS

2006 ◽  
Vol 04 (01) ◽  
pp. 59-74 ◽  
Author(s):  
YING-JUN HE ◽  
TRINH N. D. HUYNH ◽  
JESPER JANSSON ◽  
WING-KIN SUNG
Keyword(s):  
Approximation Algorithms ◽  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Phylogenetic Network ◽  
Evolutionary Relationships ◽  
Large Set ◽  
Tree Network ◽  
History Of ◽  
Overlapping Sets

To construct a phylogenetic tree or phylogenetic network for describing the evolutionary history of a set of species is a well-studied problem in computational biology. One previously proposed method to infer a phylogenetic tree/network for a large set of species is by merging a collection of known smaller phylogenetic trees on overlapping sets of species so that no (or as little as possible) branching information is lost. However, little work has been done so far on inferring a phylogenetic tree/network from a specified set of trees when in addition, certain evolutionary relationships among the species are known to be highly unlikely. In this paper, we consider the problem of constructing a phylogenetic tree/network which is consistent with all of the rooted triplets in a given set [Formula: see text] and none of the rooted triplets in another given set [Formula: see text]. Although NP-hard in the general case, we provide some efficient exact and approximation algorithms for a number of biologically meaningful variants of the problem.

Visualizing Speciation in Artificial Cichlid Fish

2006 ◽  
Vol 12 (2) ◽  
pp. 243-257 ◽  
Author(s):  
Ross Clement
Keyword(s):  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Cichlid Fish ◽  
Natural Consequence ◽  
Open Problems ◽  
Visualization System ◽  
Low Level ◽  
Wide Range ◽  
Level Information ◽  
History Of

The Cichlid Speciation Project (CSP) is an ALife simulation system for investigating open problems in the speciation of African cichlid fish. The CSP can be used to perform a wide range of experiments that show that speciation is a natural consequence of certain biological systems. A visualization system capable of extracting the history of speciation from low-level trace data and creating a phylogenetic tree has been implemented. Unlike previous approaches, this visualization system presents a concrete trace of speciation, rather than a summary of low-level information from which the viewer can make subjective decisions on how speciation progressed. The phylogenetic trees are a more objective visualization of speciation, and enable automated collection and summarization of the results of experiments. The visualization system is used to create a phylogenetic tree from an experiment that models sympatric speciation.

scholarly journals Mathematical Understanding of Sequence Alignment and Phylogenetic Algorithms: A Comprehensive Review of Methods

2020 ◽  
Author(s):  
Rashid Saif ◽  
Sadia Nadeem ◽  
Ali Iftekhar ◽  
Alishba Khaliq ◽  
Saeeda Zia
Keyword(s):  
Phylogenetic Tree ◽  
Sequence Alignment ◽  
Phylogenetic Trees ◽  
Evolutionary Relationship ◽  
Biological Sequences ◽  
Pairwise Sequence Alignment ◽  
Phylogenetic Tree Construction ◽  
Local Sequence Alignment ◽  
Tree Construction ◽  
Local Sequence

Abstract Context: Pairwise sequence alignment is one of the ways to arrange two biological sequences to identify regions of resemblance that may suggest the functional, structural, and/or evolutionary relationship (proteins or nucleic acids) between the sequences. There are two strategies in pairwise sequence alignment: Local sequence Alignment (Smith-waterman algorithm) and Global sequence Alignment (Needleman-Wunsch algorithm). In local sequence alignment, two sequences that may or may not be related are aligned to find regions of local similarities in large sequences whereas in global sequence alignment, two sequences same in length are aligned to identify conserved regions. Similarities and divergence between biological sequences identified by sequence alignment also have to be rationalized and visualized in the sense of phylogenetic trees. The phylogenetic tree construction methods are divided into distance-based and character-based methods. Evidence Acquisition: In this article, different algorithms of sequence alignment and phylogenetic tree construction were studied with examples and compared to establish the best among them to look into background of these methods for the better understanding of computational phylogenetics.Conclusions: Pairwise sequence alignment is a very important part of bioinformatics to compare biological sequences to find similarities among them. The alignment data is visualized through phylogenetic tree diagram that shows evolutionary history among organisms. Phylogenetic tree is constructed through various methods some are easier but does not provide accurate evolutionary data whereas others provide accurate evolutionary distance among organism but are computationally exhaustive.

scholarly journals Conserving the functional and phylogenetic trees of life of European tetrapods

2015 ◽  
Vol 370 (1662) ◽  
pp. 20140005 ◽  
Author(s):  
Wilfried Thuiller ◽  
Luigi Maiorano ◽  
Florent Mazel ◽  
François Guilhaumon ◽  
Gentile Francesco Ficetola ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Current System ◽  
Natura 2000 ◽  
Taxonomic Diversity ◽  
Distinct Species ◽  
Protection System ◽  
Distribution Data ◽  
History Of

Protected areas (PAs) are pivotal tools for biodiversity conservation on the Earth. Europe has had an extensive protection system since Natura 2000 areas were created in parallel with traditional parks and reserves. However, the extent to which this system covers not only taxonomic diversity but also other biodiversity facets, such as evolutionary history and functional diversity, has never been evaluated. Using high-resolution distribution data of all European tetrapods together with dated molecular phylogenies and detailed trait information, we first tested whether the existing European protection system effectively covers all species and in particular, those with the highest evolutionary or functional distinctiveness. We then tested the ability of PAs to protect the entire tetrapod phylogenetic and functional trees of life by mapping species' target achievements along the internal branches of these two trees. We found that the current system is adequately representative in terms of the evolutionary history of amphibians while it fails for the rest. However, the most functionally distinct species were better represented than they would be under random conservation efforts. These results imply better protection of the tetrapod functional tree of life, which could help to ensure long-term functioning of the ecosystem, potentially at the expense of conserving evolutionary history.

scholarly journals Study of an epidemiological profile of confirmed COVID-19 positive persons in district Kathua, Jammu and Kashmir

2021 ◽  
Author(s):  
Gurmeet Kaur ◽  
Kiran Bala ◽  
Shalli .
Keyword(s):  
Disease Surveillance ◽  
Case Fatality ◽  
Epidemiological Data ◽  
Age Group ◽  
Cure Rate ◽  
Jammu And Kashmir ◽  
Travel History ◽  
History Of ◽  
Epidemiological Profile ◽  
Epidemiological Information

Background: India recorded its first COVID-19 case on 30 January 2020. Though the early, extended nationwide lockdown of the country was implemented effectively, this alone was not sufficient to defeat the COVID-19 disease. Realizing the importance of the need to generate local epidemiological data through robust studies, this study was undertaken in a district Kathua of Jammu and Kashmir. The aim was to study the epidemiological profile of patients tested positive in district Kathua.Methods: Retrospective observational study was done to find the spatial distribution of corona virus infection in the five blocks in district Kathua of Jammu and Kashmir. Data from the integrated disease surveillance project (IDSP) unit of district Kathua was screened and the epidemiological information from all the positive reports which included the total number of COVID-19 positive cases, address, travel history, contact history were extracted for the period of five months April 2020 to August 2020.Results: 929 patients were found positive for COVID-19. Male outnumbered the females.  More than 58.8% of males were of age group 21-40 years and the least number of positive male cases were seen in the age group >80 years. In our study 627 (67%) had a history of travel, 202 (21%) had a history of contact with a positive patient, 100 (10%) were positive with no history of travel or contact.Conclusions: Kathua block of the district was maximally affected having the 58.7% largest number of COVID-19 positive cases with cure rate of 92.46% and case fatality rate of 0.5% was observed.

scholarly journals Phylogenetic Tree Construction Using K-Mer Forest- Based Distance Calculation

2020 ◽  
Vol 16 (07) ◽  
pp. 4 ◽  
Author(s):  
Gihan Gamage ◽  
Nadeeshan Gimhana ◽  
Indika Perera ◽  
Shanaka Bandara ◽  
Thilina Pathirana ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Genetic Relatedness ◽  
Biological Information ◽  
Pairwise Distance ◽  
Phylogenetic Tree Construction ◽  
Distance Calculation ◽  
Alignment Free ◽  
Tree Construction

Phylogenetics is one of the dominant data engineering research disciplines based on biological information. More particularly here, we consider raw DNA sequences and do comparative analysis in order to come up with important conclusions. When representing evolutionary relationships among different organisms in a concise manner, the phylogenetic tree helps significantly. When constructing phylogenetic trees, the elementary step is to calculate the genetic distance among species. Alignment-based sequencing and alignment-free sequencing are the two main distance computation methods that are used to find genetic relatedness of different species. In this paper we propose a novel alignment-free, pairwise, distance calculation method based on k-mers and a state of art machine learning-based phylogenetic tree construction mechanism. With the proposed approach we can convert longer DNA sequences into compendious k-mer forests which gear up the efficiency of comparison. Later we construct the phylogenetic tree based on calculated distances with the help of an algorithm build upon k-medoid clustering, which guaranteed significant efficiency and accuracy compared to traditional phylogenetic tree construction methods.

scholarly journals Comparison of Phylogenetic Tree Topologies for Nitrogen Associated Genes Partially Reconstruct the Evolutionary History of Saccharomyces cerevisiae

2019 ◽  
Vol 8 (1) ◽  
pp. 32
Author(s):  
Manuel Villalobos-Cid ◽  
Francisco Salinas ◽  
Eduardo I. Kessi-Pérez ◽  
Matteo De Chiara ◽  
Gianni Liti ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Total Evidence ◽  
Sequence Information ◽  
Phylogenetic Cluster ◽  
History Of ◽  
Tree Topologies ◽  
Yeast Genomes

Massive sequencing projects executed in Saccharomyces cerevisiae have revealed in detail its population structure. The recent “1002 yeast genomes project” has become the most complete catalogue of yeast genetic diversity and a powerful resource to analyse the evolutionary history of genes affecting specific phenotypes. In this work, we selected 22 nitrogen associated genes and analysed the sequence information from the 1011 strains of the “1002 yeast genomes project”. We constructed a total evidence (TE) phylogenetic tree using concatenated information, which showed a 27% topology similarity with the reference (REF) tree of the “1002 yeast genomes project”. We also generated individual phylogenetic trees for each gene and compared their topologies, identifying genes with similar topologies (suggesting a shared evolutionary history). Furthermore, we pruned the constructed phylogenetic trees to compare the REF tree topology versus the TE tree and the individual genes trees, considering each phylogenetic cluster/subcluster within the population, observing genes with cluster/subcluster topologies of high similarity to the REF tree. Finally, we used the pruned versions of the phylogenetic trees to compare four strains considered as representatives of S. cerevisiae clean lineages, observing for 15 genes that its cluster topologies match 100% the REF tree, supporting that these strains represent main lineages of yeast population. Altogether, our results showed the potential of tree topologies comparison for exploring the evolutionary history of a specific group of genes.

scholarly journals A CASE REPORT OF MODERATE COVID-19 AND MALARIA FALCIPARUM CO-INFECTION WITH THROMBOCYTOPENIA

2021 ◽  
Vol 8 (3) ◽  
pp. 173-178
Author(s):  
Nelda Aprilia Salim ◽  
Harun Hudari ◽  
Mega Permata ◽  
Yenny Dian Andayani ◽  
Zen Ahmad ◽  
...  
Keyword(s):  
Medical Personnel ◽  
Symptomatic Therapy ◽  
Travel History ◽  
X Ray ◽  
Normal Limits ◽  
Appropriate Treatment ◽  
The World ◽  
History Of ◽  
Chest X Ray ◽  
D Dimer

The COVID-19 pandemic that attacks the world has made the attention of all medical personnel focused on this disease. The clinical picture is similar to other infectious diseases such as malaria, dengue, influenza, etc., which often leads to misdiagnosis. We report the case of a man, 31 years old, with a history of travel and complaints of high fever persisting for more than 7 days. On physical examination, the temperature was 39-40 C, others were within normal limits. Initial platelet count was 69 x 103/µL, leukocytes was 15.52 x 109/L, CRP was 96 mg/L. The blood smear found Plasmodium falciparum, and PCR SARS-CoV-2 was positive. Chest X-ray showed pneumonia. Dihydroartemisinin-piperaquine and primaquine therapies were administered for malaria, as well as favipiravir, azithromycin, and other symptomatic therapy for COVID-19. Platelets decreased to 38 x 103/µL while D-dimer level increased (> 20 mg/L). Anticoagulant was delayed. On monitoring after therapy, the platelets returned to normal, the D-dimer level decreased, and there was no bleeding. The co-infectious conditions of malaria and COVID-19 should be suspected in patients with suggestive symptoms and travel history from endemic areas, therefore both examinations should be performed. This co-infection has the potential to cause hyper inflammation and hypercoagulation and this is associated with a poor prognosis. Appropriate treatment is needed.

scholarly journals Annotated catalog and bibliography of the cyclocephaline scarab beetles (Coleoptera, Scarabaeidae, Dynastinae, Cyclocephalini)

ZooKeys ◽  
2018 ◽  
Vol 745 ◽  
pp. 101-378 ◽  
Author(s):  
Matthew R. Moore ◽  
Ronald D. Cave ◽  
Marc A. Branham
Keyword(s):  
Research Interest ◽  
Distribution Data ◽  
The World ◽  
History Of ◽  
Annotated Catalog ◽  
Nomen Novum ◽  
Exhaustive List ◽  
Scarab Beetles

Cyclocephaline scarab beetles represent the second largest tribe of the subfamily Dynastinae, and the group includes the most speciose genus of dynastines, Cyclocephala. The period following publication of Sebő Endrődi’s The Dynastinae of the World has seen a huge increase in research interest on cyclocephalines, and much of this research has not been synthesized. The objective of this catalog and bibliography is to compile an exhaustive list of taxa in Cyclocephalini. This paper provides an updated foundation for understanding the taxonomy and classification of 14 genera and over 500 species in the tribe. It discusses the history of cataloging dynastine species, clarifies issues surrounding the neotype designations in Endrődi’s revision of Cyclocephalini, synthesizes all published distribution data for cyclocephaline species, and increases accessibility to the voluminous literature on the group by providing an easily searchable bibliography for each species. We propose the nomen novum Cyclocephalarogerpauli, new replacement name, for C.nigra Dechambre.

scholarly journals A Covariance Matrix Inversion Problem arising from the Construction of Phylogenetic Trees

2007 ◽  
Vol 10 ◽  
pp. 119-131
Author(s):  
Tom M. W. Nye ◽  
Brad J. C. Baxter ◽  
Walter R. Gilks
Keyword(s):  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Symmetric Matrix ◽  
Matrix Inversion ◽  
Covariance Matrices ◽  
Inner Product ◽  
Inversion Problem ◽  
Inversion Algorithm ◽  
Tree Construction ◽  
Under Construction

AbstractWe describe an efficient algorithm for the inversion of covariance matrices that arise in the context of phylogenetic tree construction. Phylogenetic trees describe the evolutionary relationships between species, and their construction is computationally demanding. Many approaches involve the symmetric matrix of evolutionary distances between species. Regarding these distances as random variables, the corresponding set of variances and covariances form a rank-4 tensor, and the inner-product defined by its inverse can be used to assign statistical scores to candidate trees. We describe a natural set of assumptions for the phylogenetic tree under construction, and show how under these assumptions the covariance tensor for a tree with n leaves can be inverted in O(n2) operations. In addition to presenting the inversion algorithm, we hope this article will open algebraic and computational problems from the field of phylogeny to a wider audience.

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